[English] 日本語
Yorodumi
- PDB-5nvk: Crystal structure of the human 4EHP-GIGYF1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nvk
TitleCrystal structure of the human 4EHP-GIGYF1 complex
Components
  • Eukaryotic translation initiation factor 4E type 2
  • GRB10-interacting GYF protein 1
KeywordsTRANSLATION / translational regulation / cap-binding protein / 4EHP-binding protein / GRB10-interacting GYF protein 1
Function / homology
Function and homology information


RNA cap binding / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding / negative regulation of type I interferon-mediated signaling pathway / negative regulation of translational initiation / translation initiation factor activity / rescue of stalled cytosolic ribosome ...RNA cap binding / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding / negative regulation of type I interferon-mediated signaling pathway / negative regulation of translational initiation / translation initiation factor activity / rescue of stalled cytosolic ribosome / insulin-like growth factor receptor signaling pathway / translational initiation / P-body / ISG15 antiviral mechanism / negative regulation of translation / ubiquitin protein ligase binding / protein-containing complex / RNA binding / cytosol / cytoplasm
Similarity search - Function
: / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. ...: / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 4E type 2 / GRB10-interacting GYF protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPeter, D. / Valkov, E.
CitationJournal: Genes Dev. / Year: 2017
Title: GIGYF1/2 proteins use auxiliary sequences to selectively bind to 4EHP and repress target mRNA expression.
Authors: Peter, D. / Weber, R. / Sandmeir, F. / Wohlbold, L. / Helms, S. / Bawankar, P. / Valkov, E. / Igreja, C. / Izaurralde, E.
History
DepositionMay 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E type 2
B: GRB10-interacting GYF protein 1
C: Eukaryotic translation initiation factor 4E type 2
D: GRB10-interacting GYF protein 1
E: Eukaryotic translation initiation factor 4E type 2
F: GRB10-interacting GYF protein 1
G: Eukaryotic translation initiation factor 4E type 2
H: GRB10-interacting GYF protein 1


Theoretical massNumber of molelcules
Total (without water)122,8488
Polymers122,8488
Non-polymers00
Water00
1
A: Eukaryotic translation initiation factor 4E type 2
B: GRB10-interacting GYF protein 1


Theoretical massNumber of molelcules
Total (without water)30,7122
Polymers30,7122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-28 kcal/mol
Surface area13030 Å2
MethodPISA
2
C: Eukaryotic translation initiation factor 4E type 2
D: GRB10-interacting GYF protein 1


Theoretical massNumber of molelcules
Total (without water)30,7122
Polymers30,7122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-23 kcal/mol
Surface area13810 Å2
MethodPISA
3
E: Eukaryotic translation initiation factor 4E type 2
F: GRB10-interacting GYF protein 1


Theoretical massNumber of molelcules
Total (without water)30,7122
Polymers30,7122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-26 kcal/mol
Surface area12530 Å2
MethodPISA
4
G: Eukaryotic translation initiation factor 4E type 2
H: GRB10-interacting GYF protein 1


Theoretical massNumber of molelcules
Total (without water)30,7122
Polymers30,7122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-28 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.320, 135.320, 60.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

-
Components

#1: Protein
Eukaryotic translation initiation factor 4E type 2 / eIF4E type 2 / Eukaryotic translation initiation factor 4E homologous protein / Eukaryotic ...eIF4E type 2 / Eukaryotic translation initiation factor 4E homologous protein / Eukaryotic translation initiation factor 4E-like 3 / eIF4E-like protein 4E-LP / mRNA cap-binding protein 4EHP / h4EHP / mRNA cap-binding protein type 3


Mass: 21979.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: the first residue of the coordinate sequence of chain G belongs to the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E2, EIF4EL3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: O60573
#2: Protein
GRB10-interacting GYF protein 1 / PERQ amino acid-rich with GYF domain-containing protein 1


Mass: 8732.963 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GIGYF1, CDS2, PERQ1, PP3360 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: O75420

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350 0.2 M KCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99981 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99981 Å / Relative weight: 1
ReflectionResolution: 2.9→47.843 Å / Num. obs: 24699 / % possible obs: 99.6 % / Redundancy: 3.4 % / Rsym value: 0.111 / Net I/σ(I): 10.9
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.95 / Num. unique all: 1782 / Rsym value: 0.647 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NVL

5nvl


Resolution: 2.9→47.843 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.07
RfactorNum. reflection% reflectionSelection details
Rfree0.2538 1218 4.93 %Random selection
Rwork0.2042 ---
obs0.2067 24694 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.4 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7833 0 0 0 7833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038014
X-RAY DIFFRACTIONf_angle_d0.49410834
X-RAY DIFFRACTIONf_dihedral_angle_d16.4554839
X-RAY DIFFRACTIONf_chiral_restr0.0391152
X-RAY DIFFRACTIONf_plane_restr0.0031404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.01620.32061300.28872564X-RAY DIFFRACTION100
3.0162-3.15350.35211280.25982628X-RAY DIFFRACTION100
3.1535-3.31970.32821420.25782555X-RAY DIFFRACTION100
3.3197-3.52760.28861470.2382582X-RAY DIFFRACTION100
3.5276-3.79990.27121390.21522607X-RAY DIFFRACTION100
3.7999-4.18210.24521390.1962572X-RAY DIFFRACTION100
4.1821-4.78680.20281320.16732625X-RAY DIFFRACTION99
4.7868-6.02890.21541380.1752621X-RAY DIFFRACTION100
6.0289-47.84930.2231230.17892722X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2925-0.0402-0.0741.5824-0.06650.38050.03660.09950.0666-0.1059-0.01330.19340.0238-0.11340.00260.4310.026-0.01540.46770.0190.1218-10.992316.3599-38.3102
22.1754-0.8313-0.18351.801-0.33121.5434-0.1559-0.13380.08620.28260.11660.1999-0.0965-0.27110.02790.5145-0.04630.04510.3997-0.01860.1786-14.053424.4844-28.238
32.99980.0895-0.54352.33130.43292.98290.1877-0.06070.4891-0.04370.0364-0.3584-0.51570.13-0.14680.45490.00340.08810.3089-0.04580.31645.841748.6068-28.1842
42.7799-0.04210.50391.46460.6771.57070.21150.04980.25580.24860.0391-0.4911-0.0930.115-0.30350.5794-0.04910.01630.4683-0.00170.31717.761338.7647-35.1999
51.4576-0.112-0.1192.28940.03831.5892-0.144-0.35860.05840.48190.18590.3288-0.1073-0.30060.09970.51690.09620.03860.6521-0.08260.191619.42976.7465-1.2315
61.0252-0.13480.46730.40510.27680.9839-0.255-0.27160.33050.61890.0819-0.1172-0.22840.273-0.10170.66780.0605-0.07590.5816-0.10330.265630.375481.668-6.0963
72.7707-0.06250.29480.2239-0.04751.1649-0.10670.1509-0.2906-0.05650.1239-0.01920.15230.05260.00050.4384-0.00430.01850.3824-0.06640.182650.509357.9738-10.0165
82.2787-0.44140.22550.4524-0.05191.50260.0174-0.4758-0.50280.0976-0.05890.1580.2921-0.04290.06250.5198-0.03530.04620.52430.05140.232842.254955.25380.2461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 52 through 232)
2X-RAY DIFFRACTION2(chain 'B' and resid 36 through 103)
3X-RAY DIFFRACTION3(chain 'C' and resid 52 through 219)
4X-RAY DIFFRACTION4(chain 'D' and resid 30 through 103)
5X-RAY DIFFRACTION5(chain 'E' and resid 52 through 219)
6X-RAY DIFFRACTION6(chain 'F' and resid 37 through 103)
7X-RAY DIFFRACTION7(chain 'G' and resid 51 through 233)
8X-RAY DIFFRACTION8(chain 'H' and resid 38 through 103)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more